--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/medaka_variant.xml	Sat May 23 13:37:48 2020 -0400
@@ -0,0 +1,159 @@
+<tool id="medaka_variant_pipeline" name="medaka: Variant pipeline" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+    <description>via neural networks</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="exit_code"><![CDATA[
+        ## initialize
+        @REF_FASTA@  
+        ## link doesn't work
+        cp '${i}' 'alignment.bam' &&
+        cp '${i.metadata.bam_index}' 'alignment.bam.bai' &&
+
+        ## run
+        medaka_variant
+        ## optional
+        #if str($r) != ''
+            -r '$r'
+        #end if
+        -o 'results'
+        -s '$s'
+        -m '$m'
+        -t \${GALAXY_SLOTS:-4}
+        -b $b
+        -N $N
+        -P $P
+        $U
+        $S
+        ## required
+        -i 'alignment.bam'
+        -f 'reference.fa'
+
+        |& tee 'log.txt'
+    ]]></command>
+    <inputs>
+        <param argument="-i" type="data" format="bam" label="Select input reads" help="Read groups are currently ignored, so the bam should only contain reads from a single sample."/>
+        <expand macro="reference"/>
+        <param argument="-r" type="text" value="" optional="true" label="Set region string(s)" help="If not provided, will process all contigs."/>
+        <expand macro="model" argument="-s" label="Select model for initial SNP calling from mixed reads prior to phasing"/>
+        <expand macro="model" argument="-m" label="Select model for final variant calling from phased reads"/>
+        <expand macro="b"/>
+        <param argument="-N" type="integer" value="14" label="Set threshold for filtering indels in final VCF"/>
+        <param argument="-P" type="integer" value="12" label="Set threshold for filtering SNPs in final VCF"/>
+        <param argument="-U" type="boolean" truevalue="-U" falsevalue="" label="Avoid filtering of final VCF?"/>
+        <param argument="-S" type="boolean" truevalue="-S" falsevalue="" label="Stop after initial SNP calling from mixed reads prior to phasing?"/>
+        <param name="out" type="select" multiple="true" optional="false" label="Select out file(s)5">
+            <option value="round_0_hap_mixed_phased_bam">round_0_hap_mixed_phased.bam</option>
+            <option value="round_0_hap_mixed_phased_vcf">round_0_hap_mixed_phased.vcf</option>
+            <option value="round_0_hap_mixed_probs_hdf">round_0_hap_mixed_probs.hdf</option>
+            <option value="round_0_hap_mixed_unphased_vcf">round_0_hap_mixed_unphased.vcf</option>
+            <option value="round_1_hap_1_vcf">round_1_hap_1.vcf</option>
+            <option value="round_1_hap_2_vcf">round_1_hap_2.vcf</option>
+            <option value="round_1_hap_1_probs_hdf">round_1_hap_1_probs.hdf</option>
+            <option value="round_1_hap_2_probs_hdf">round_1_hap_2_probs.hdf</option>
+            <option value="round_1_unfiltered_vcf">round_1_unfiltered.vcf</option>
+            <option value="round_1_vcf" selected="true">round_1.vcf</option>
+            <option value="log">Log</option>
+        </param>
+    </inputs>
+    <outputs>
+        <!-- standard -->
+        <data name="out_round_1_vcf" format="vcf" label="${tool.name} on ${on_string}: round_1.vcf" from_work_dir="results/round_1.vcf">
+            <filter>'round_1_vcf' in out</filter>
+        </data>
+        <!-- optional -->
+        <data name="out_round_0_hap_mixed_probs_hdf" format="h5" label="${tool.name} on ${on_string}: round_0_hap_mixed_probs_hdf" from_work_dir="results/round_0_hap_mixed_probs.hdf">
+            <filter>'round_0_hap_mixed_probs_hdf' in out</filter>
+        </data>
+        <data name="out_round_0_hap_mixed_phased_bam" format="bam" label="${tool.name} on ${on_string}: round_0_hap_mixed_phased_bam" from_work_dir="results/round_0_hap_mixed_phased.bam">
+            <filter>'round_0_hap_mixed_phased_bam' in out</filter>
+        </data>
+        <data name="out_round_0_hap_mixed_phased_vcf" format="vcf" label="${tool.name} on ${on_string}: round_0_hap_mixed_phased_vcf" from_work_dir="results/round_0_hap_mixed_phased.vcf">
+            <filter>'round_0_hap_mixed_phased_vcf' in out</filter>
+        </data>
+        <data name="out_round_0_hap_mixed_unphased_vcf" format="vcf" label="${tool.name} on ${on_string}: round_0_hap_mixed_unphased_vcf" from_work_dir="results/round_0_hap_mixed_unphased.vcf">
+            <filter>'round_0_hap_mixed_unphased_vcf' in out</filter>
+        </data>
+        <!-- round 1 -->
+        <data name="out_round_1_hap_1_vcf" format="vcf" label="${tool.name} on ${on_string}: round_1_hap_1.vcf" from_work_dir="results/round_1_hap_1.vcf">
+            <filter>'round_1_hap_1_vcf' in out</filter>
+        </data>
+        <data name="out_round_1_hap_1_probs_hdf" format="h5" label="${tool.name} on ${on_string}: round_1_hap_1_probs.hdf" from_work_dir="results/round_1_hap_1_probs.hdf">
+            <filter>'round_1_hap_1_probs_hdf' in out</filter>
+        </data>
+        <data name="out_round_1_hap_2_vcf" format="vcf" label="${tool.name} on ${on_string}: round_1_hap_2.vcf" from_work_dir="results/round_1_hap_2.vcf">
+            <filter>'round_1_hap_2_vcf' in out</filter>
+        </data>
+        <data name="out_round_1_hap_2_probs_hdf" format="h5" label="${tool.name} on ${on_string}: round_1_hap_2_probs.hdf" from_work_dir="results/round_1_hap_2_probs.hdf">
+            <filter>'round_1_hap_2_probs_hdf' in out</filter>
+        </data>
+        <data name="out_round_1_unfiltered_vcf" format="vcf" label="${tool.name} on ${on_string}: round_1_unfiltered.vcf" from_work_dir="results/round_1_unfiltered.vcf">
+            <filter>'round_1_unfiltered_vcf' in out</filter>
+        </data>
+        <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="log.txt">
+            <filter>'log' in out</filter>
+        </data>
+    </outputs>
+    <tests>
+        <!-- #1 default -->
+        <test>
+            <param name="i" value="alignment.bam"/>
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="cached"/>
+                <param name="ref_file" value="bwa-mem-mt-genome"/>
+            </conditional>
+            <param name="out" value="round_0_hap_mixed_probs.hdf,round_0_hap_mixed_unphased.vcf,log"/>
+            <output name="out_round_0_hap_mixed_unphased_vcf">
+                <assert_contents>
+                    <has_n_lines n="6"/>
+                    <has_line line="##fileformat=VCFv4.1"/>
+                </assert_contents>
+            </output>
+            <output name="out_round_0_hap_mixed_probs_hdf">
+                <assert_contents>
+                    <has_size value="32624"/>
+                </assert_contents>
+            </output>
+            <output name="out_log">
+                <assert_contents>
+                    <has_line line="++ Preparing data"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+@WID@
+
+The module *medaka_variant* performs a variant calling via neural networks.
+
+**Input**
+
+It is unlikely that the model arguments should be changed from their defaults.
+
+- reads aligned to reference (BAM), should be aligned to the reference against which to call variants
+- reference (FASTA)
+
+**Output**
+
+- round_0_hap_mixed_phased.vcf
+- round_0_hap_mixed_probs.hdf
+- round_0_hap_mixed_unphased.vcf
+- round_1_hap_1_probs.hdf
+- round_1_hap_1.vcf
+- round_1_hap_2_probs.hdf
+- round_1_hap_2.vcf
+- round_1_unfiltered.vcf
+- round_1.vcf
+
+**References**
+
+@REFERENCES@
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
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